Dirt: Biogeography of the Pacific Crest Trail

This is a collaborative project by Christina Agapakis and Ellie Harmon, supported by the University of California Institute for Research in the Arts. While hiking the Pacific Crest Trail, Ellie collected samples of dirt throughout California and sent them to Christina's lab. They extracted DNA from the bacteria living in the dirt and sequenced the 16S ribosomal RNA to identify what species of bacteria were there. Click on a name to see a summary of where we found that genus of bacteria.

Acidobacteria

Acidobacteriaceae (Unknown genus)
Acidobacterium
Edaphobacter
Geothrix
Holophaga
Koribacter
Solibacter
Terriglobus
Unknown Acidobacteria

Actinobacteria

Acidimicrobium
Actinoallomurus
Actinocatenispora
Actinomycetales (Unknown order and genus)
Actinoplanes
Actinospica
Aeromicrobium
Agromyces
Amycolatopsis
Arthrobacter
Blastococcus
Cellulosimicrobium
Conexibacter
Corynebacterium
Cryptosporangium
Curtobacterium
Dactylosporangium
Frankia
Friedmanniella
Geodermatophilaceae (Unknown genus)
Geodermatophilus
Iamia
Ilumatobacter
Intrasporangiaceae (Unknown genus)
Janibacter
Jiangella
Kineococcus
Kineosporia
Kocuria
Kribbella
Microbacteriaceae (Unknown genus)
Microbacterium
Micrococcaceae (Unknown genus)
Microlunatus
Micromonospora
Micromonosporaceae (Unknown genus)
Modestobacter
Mycobacterium
Nakamurella
Nakamurellaceae (Unknown genus)
Nocardiaceae (Unknown genus)
Nocardioidaceae (Unknown genus)
Nocardioides
Patulibacter
Propionibacteriaceae (Unknown genus)
Propionibacterium
Pseudonocardia
Pseudonocardiaceae (Unknown genus)
Rhodococcus
Rubrobacter
Saccharopolyspora
Solirubrobacter
Solirubrobacterales (Unknown order and genus)
Sporichthya
Streptomyces
Streptomycetaceae (Unknown genus)
Streptosporangiaceae (Unknown genus)
Streptosporangium
Tetrasphaera
Thermoleophilum
Thermomonospora
Thermomonosporaceae (Unknown genus)
Unknown Actinobacteria

Bacteroidetes

Adhaeribacter
Alkaliflexus
Aquiflexum
Arcicella
Bacteroidales (Unknown order and genus)
Bacteroides
Chitinophaga
Chitinophagaceae (Unknown genus)
Chryseobacterium
Crocinitomix
Cytophaga
Cytophagaceae (Unknown genus)
Cytophagales (Unknown order and genus)
Dyadobacter
Emticicia
Flavisolibacter
Flavobacteriaceae (Unknown genus)
Flavobacteriales (Unknown order and genus)
Flavobacterium
Flexibacter
Flexithrix
Fluviicola
Haliscomenobacter
Hymenobacter
Larkinella
Mucilaginibacter
Niastella
Pedobacter
Petrimonas
Pontibacter
Porphyromonas
Proteiniphilum
Rhodothermus
Runella
Segetibacter
Solibium
Sphingobacteriaceae (Unknown genus)
Sphingobacteriales (Unknown order and genus)
Sphingobacterium
Sphingoterrabacterium
Spirosoma
Sporocytophaga
Terrimonas
Unknown Bacteroidetes

Chlamydiae

Neochlamydia

Chloroflexi

Anaerolinea
Anaerolineaceae (Unknown genus)
Bellilinea
Caldilinea
Chloroflexales (Unknown order and genus)
Chloroflexus
Herpetosiphon
Kouleothrix
Ktedonobacter
Ktedonobacterales (Unknown order and genus)
Levilinea
Oscillochloris
Roseiflexus
Sphaerobacter
Thermomicrobium
Thermosporothrix
Unknown Chloroflexi

Cyanobacteria

Aphanizomenon
Chamaesiphon
Chroococcales(family) (Unknown genus)
Chroococcus
Cyanobacterium
Cyanobacteria (Unknown order and genus)
Leptolyngbya
Microcystis
Nostoc
Nostocaceae
Nostocaceae (Unknown genus)
Nostocales (Unknown order and genus)
Oscillatoriales(family) (Unknown genus)
Phormidium
Pleurocapsales(family) (Unknown genus)
Prochloron
Unknown Cyanobacteria

Deinococcus-Thermus

Deinococcus
Marinithermus
Thermus
Truepera


Fibrobacteres

Fibrobacter

Firmicutes

Acetivibrio
Alicyclobacillus
Ammoniphilus
Aneurinibacillus
Bacillaceae (Unknown genus)
Bacillales (Unknown order and genus)
Bacillus
Brevibacillus
CandidatusArthromitus
Carnobacteriaceae (Unknown genus)
Carnobacterium
Clostridiaceae (Unknown genus)
Clostridiales (Unknown order and genus)
Clostridium
Erysipelothrix
Eubacterium
Exiguobacterium
Faecalibacterium
Fusibacter
Gelria
Halothermothrix
Holdemania
Laceyella
Lactobacillus
Paenibacillaceae (Unknown genus)
Paenibacillus
Planococcaceae (Unknown genus)
Planococcus
Sporobacter
Sporobacterium
Sporosarcina
Sporotalea
Staphylococcus
Thermacetogenium
Thermoactinomycetaceae (Unknown genus)
Thermodesulfobium
Turicibacter
Ureibacillus
Unknown Firmicutes

Fusobacteria

Fusobacteriaceae (Unknown genus)

Gemmatimonadetes

Gemmatimonas

Lentisphaerae

Victivallis

Nitrospirae

Magnetobacterium
Nitrospira

Planctomycetes

Gemmata
Nostocoida(Planctomycetales)
Phycisphaera
Pirellula
Planctomyces
Planctomycetaceae (Unknown genus)
Planctomycetales (Unknown order and genus)
Unknown Planctomycetes

Proteobacteria

Acetobacter
Acetobacteraceae (Unknown genus)
Achromobacter
Acidiphilium
Acidisphaera
Acidocella
Acidomonas
Acinetobacter
Aeromonas
Agrobacterium
Alcaligenaceae (Unknown genus)
Alkanindiges
Alphaproteobacteria(family) (Unknown genus)
Amaricoccus
Anaeromyxobacter
Anaplasma
Aquabacterium
Aquamonas
Aquicella
Aquimonas
Arcobacter
Azonexus
Azospira
Azospirillum
Bacteriovoracaceae (Unknown genus)
Bacteriovorax
Bdellovibrio
Bdellovibrionales (Unknown order and genus)
Beggiatoa
Beijerinckiaceae (Unknown genus)
Blastochloris
Bosea
Bradyrhizobiaceae (Unknown genus)
Bradyrhizobium
Brevundimonas
Brucellaceae (Unknown genus)
Burkholderia
Burkholderiaceae (Unknown genus)
Burkholderiales (Unknown order and genus)
Burkholderiales(family) (Unknown genus)
Byssovorax
Captivus
Caulobacter
Caulobacteraceae (Unknown genus)
Cellvibrio
Chelatococcus
Chitinimonas
Chondromyces
Comamonadaceae (Unknown genus)
Coxiella
Cupriavidus
Dechloromonas
Deefgea
Defluviicoccus
Delftia
Derxia
Desulfobacca
Desulfofustis
Desulforegula
Desulforhabdus
Devosia
Dokdonella
Duganella
Dyella
Ectothiorhodospiraceae (Unknown genus)
Enterobacteriaceae (Unknown genus)
Entotheonella
Erythrobacter
Erythrobacteraceae (Unknown genus)
Escherichia
Geobacter
Geobacteraceae (Unknown genus)
Geopsychrobacter
Gluconacetobacter
Gluconobacter
Haliangium
Halomonas
Helicobacter
Herbaspirillum
Hippea
Hydrogenophaga
Hylemonella
Hyphomicrobiaceae (Unknown genus)
Hyphomicrobium
Ideonella
Inquilinus
Janthinobacterium
Kaistibacter
Kingella
Kofleria
Kozakia
Labrys
Legionella
Legionellales (Unknown order and genus)
Liberibacter
Lysobacter
Macromonas
Magnetospirillum
Malonomonas
Massilia
Mesorhizobium


Proteobacteria cont.

Methylobacter
Methylobacteriaceae (Unknown genus)
Methylobacterium
Methylocapsa
Methylocystaceae (Unknown genus)
Methylocystis
Methylomicrobium
Methylophilaceae (Unknown genus)
Methylophilus
Methylosinus
Methylothermus
Micavibrio
Microbulbifer
Microvirga
Moraxella
Moraxellaceae (Unknown genus)
Myxococcaceae (Unknown genus)
Myxococcales (Unknown order and genus)
Nannocystis
Neisseriaceae (Unknown genus)
Nisaea
Nitratireductor
Nitrosomonas
Nitrosospira
Nitrosovibrio
Novosphingobium
Oceanicola
Ochrobactrum
Odyssella
Oleomonas
Oxalobacteraceae (Unknown genus)
Pantoea
Paracoccus
Paracraurococcus
Parvibaculum
Parvularcula
Paucibacter
Paucimonas
Pelobacter
Pelomonas
Perlucidibaca
Phaeospirillum
Phenylobacterium
Phyllobacteriaceae (Unknown genus)
Pleomorphomonas
Polyangiaceae (Unknown genus)
Polynucleobacter
Porphyrobacter
Pseudaminobacter
Pseudomonadaceae (Unknown genus)
Pseudomonadales (Unknown order and genus)
Pseudomonas
Pseudovibrio
Psychrobacter
Rahnella
Ralstonia
Rheinheimera
Rhizobiaceae (Unknown genus)
Rhizobiales (Unknown order and genus)
Rhizobium
Rhodobacter
Rhodobacteraceae (Unknown genus)
Rhodobacterales (Unknown order and genus)
Rhodocista
Rhodocyclaceae (Unknown genus)
Rhodocyclus
Rhodomicrobium
Rhodopila
Rhodopseudomonas
Rhodospirillaceae (Unknown genus)
Rhodospirillales (Unknown order and genus)
Rhodovibrio
Rickettsia
Rickettsiella
Roseococcus
Roseomonas
Rubellimicrobium
Saccharospirillum
Schlegelella
Serratia
Silvimonas
Sinorhizobium
Smithella
Sorangium
Sphingobium
Sphingomonadaceae (Unknown genus)
Sphingomonadales (Unknown order and genus)
Sphingomonas
Sphingopyxis
Stella
Stenotrophomonas
Steroidobacter
Stigmatella
Sulfurospirillum
Thauera
Thiobacillus
Thiobacter
Thiorhodospira
Tistrella
Vampirovibrio
Variovorax
Vogesella
Wolinella
Xanthomonadaceae (Unknown genus)
Xanthomonadales (Unknown order and genus)
Xanthomonas
Zoogloea
Unknown Alphaproteobacteria
Unknown Betaproteobacteria
Unknown Gammaproteobacteria
Unknown Deltaproteobacteria
Unknown Proteobacteria

TM7

TM7(genus)

Tenericutes

Mollicutes(genus)

Unknown

Unknown Unknown

Verrucomicrobia

Chthoniobacter
Haloferula
Opitutus
Unknown Verrucomicrobia
Verrucomicrobiaceae (Unknown genus)
Verrucomicrobium

NoHit

NoHit